Anyways thanks for ur detailed answers .. After completing the simulation , the 10ns one I will get back to u if any doubt arises .. Also I am running a 3ns simulation of the same variant of GFP but with a different FF ... hoping to get any positive result for that one ...
On Wed, Feb 2, 2011 at 5:54 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > bharat gupta wrote: > >> Sorry to make this point here but running a 50ns simulation will take >> roughly 1 month on my system but a 10ns simulation will take 5 days on >> > > A month is a reasonable time investment for quality MD simulations. > > > my system .. so would a 10ns be enough to monitor such motions .. also i >> > > Very doubtful, but I'm not going to speculate further. You have to be > willing to put in significant effort to answer complex questions, unless > you're happy to settle for potentially unreliable data. > > > request to u guide me to a link where I can find more about this >> independent simulation and how to run many replicates & analyze them ?? >> > > There's nothing left to say. I've told you how to initiate independent > simulations. Analyzing them is up to you based on your plans for this > project. No one on this list is going to provide you broad-reaching > how-to's for doing anything you might come up with. The manual is > extensive, and the website/wiki has lots of tips and information. > > -Justin > > ..... >> On Wed, Feb 2, 2011 at 5:42 AM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> bharat gupta wrote: >> >> Sorry to ask this question but setting the gen_vel=yes and >> gen_seed = -1 will eventually lead to different simulation and >> thus different simulated structures ?? .. and after completing >> one set of simulation with this paramter and 3ns time .. do i >> have to repeat it some 3 or more times ??.... pls comment.. as >> I am going to start simulation with these parameters. >> >> >> As I have already said, the combination of velocity generation with >> a different random seed will give you (in theory) independent >> trajectories. How many replicates you run is up to you. I >> certainly hope that, after all I've said, you're still not intending >> on simply running 3-ns simulations, regardless of how many >> replicates you run. If you're looking at loop movements, you won't >> answer your questions with such little data. >> >> -Justin >> >> On Wed, Feb 2, 2011 at 5:27 AM, Justin A. Lemkul >> <jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >> >> >> >> bharat gupta wrote: >> >> Thanks for such a detailed reply to my queries .. But >> conducting >> a 50ns simulation will take time ... so i want to conduct >> independent simulation and for that I searched some >> threads but >> was not able to get the proper description and method... if >> u >> can guide me through an appropriate link .. it would be much >> more helpful .. >> >> >> Each simulation begins with the assignment of random velocities >> (gen_vel = yes). Specify different values of gen_seed (or >> leave it >> set to -1) to get different velocities each time. >> >> -Justin >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540) >> >> 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>> >> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www >> interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> >> -- Bharat >> Ph.D. Candidate >> Room No. : 7202A, 2nd Floor >> Biomolecular Engineering Laboratory >> Division of Chemical Engineering and Polymer Science >> Pusan National University >> Busan -609735 >> South Korea >> Lab phone no. - +82-51-510-3680, +82-51-583-8343 >> Mobile no. - 010-5818-3680 >> E-mail : monu46...@yahoo.com <mailto:monu46...@yahoo.com> >> <mailto:monu46...@yahoo.com <mailto:monu46...@yahoo.com>> >> >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> >> -- >> Bharat >> Ph.D. Candidate >> Room No. : 7202A, 2nd Floor >> Biomolecular Engineering Laboratory >> Division of Chemical Engineering and Polymer Science >> Pusan National University >> Busan -609735 >> South Korea >> Lab phone no. - +82-51-510-3680, +82-51-583-8343 >> Mobile no. - 010-5818-3680 >> E-mail : monu46...@yahoo.com <mailto:monu46...@yahoo.com> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists